The small bowel microbiota

Current Opinion in Gastroenterology

Volumn 31, Issue 2, 2015, Pages 130-136

  Moran, Carthage ^a   Sheehan, Donal ^a   Shanahan, Fergus ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b University College Cork and INFANT Centre   (Ireland)

Author keywords

Celiac disease; Crohn's disease; Motility; Mucosal immunity; Obesity

Indexed keywords

ANTIBIOTIC AGENT;

CELIAC DISEASE; COLON FLORA; CROHN DISEASE; DIET; HOST; HUMAN; INFLAMMATORY BOWEL DISEASE; INTESTINE MOTILITY; JET LAG; MALIGNANT NEOPLASTIC DISEASE; MICROBIOME; NONHUMAN; REVIEW; SMALL INTESTINE; HOMEOSTASIS; HOST PATHOGEN INTERACTION; IMMUNOLOGY; INNATE IMMUNITY; MICROFLORA; PATHOLOGY;

HOMEOSTASIS; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNITY, INNATE; INFLAMMATORY BOWEL DISEASES; INTESTINE, SMALL; MICROBIOTA;

EID: 84922706308     PISSN: 02671379     EISSN: 15317056     Source Type: Journal    
DOI: 10.1097/MOG.0000000000000157     Document Type: Review

References (75)

1. Johansson ME, Larsson JM, Hansson GC. The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of hostmicrobial interactions. Proc Natl Acad Sci U S A 2011; 108 (Suppl 1):4659-4665.
2. Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science 2012; 336:1268-1273.
3. Mowat AM, Agace WW. Regional specialization within the intestinal immune system. Nat Rev Immunol 2014; 14:667-685.
4. Zoetendal EG, Raes J, van den Bogert B, et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 2012; 6:1415-1426.
5. Virgin HW. The virome in mammalian physiology and disease. Cell 2014;157:142-150.
6. Kernbauer E, Ding Y, Cadwell K. An enteric virus can replace the beneficial function of commensal bacteria. Nature 2014; 516:94-98.
7. Shanahan F. The gut microbiota-a clinical perspective on lessons learned. Nat Rev Gastroenterol Hepatol 2012; 9:609-614.
8. Sommer F, Backhed F. The gut microbiota: masters of host development and physiology. Nat Rev Microbiol 2013; 11:227-238.
9. Arrieta MC, Stiemsma LT, Amenyogbe N, et al. The intestinal microbiome in early life: health and disease. Front Immunol 2014; 5:427.
10. Aidy SE, van den Bogert B, Kleerebezem M. The small intestine microbiota, nutritional modulation and relevance for health. Curr Opin Biotechnol 2014; 32C:14-20.
11. Fraher MH, O'Toole PW, Quigley EM. Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 2012; 9:312-322.
12. Goodrich JK, Di Rienzi SC, Poole AC, et al. Conducting a microbiome study. Cell 2014; 158:250-262.
13. Muller PA, Koscso B, Rajani GM, et al. Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility. Cell 2014; 158:300-313.
14. Shanahan F, O'Toole PW. Host-microbe interactions and spatial variation of cancer in the gut. Nat Rev Cancer 2014; 14:511-512.
15. Viaud S, Saccheri F, Mignot G, et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 2013; 342:971-976.
16. Iida N, Dzutsev A, Stewart CA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science 2013; 342:967-970.
17. Sistigu A, Yamazaki T, Vacchelli E, et al. Cancer cell-autonomous contribution of type I interferon signaling to the efficacy of chemotherapy. Nat Med 2014; 20:1301-1309.
18. Thaiss CA, Zeevi D, Levy M, et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell 2014; 159:514-529.
19. Schnabl B, Brenner DA. Interactions between the intestinal microbiome and liver diseases. Gastroenterology 2014; 146:1513-1524.
20. Yan AW, Fouts DE, Brandl J, et al. Enteric dysbiosis associated with a mouse model of alcoholic liver disease. Hepatology 2011; 53:96-105.
21. Chen P, Starkel P, Turner JR, et al. Dysbiosis-induced intestinal inflammation activates TNFRI and mediates alcoholic liver disease in mice. Hepatology 2014. [Epub ahead of print]
22. Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci 2012; 13:701-712.
23. Leclercq S, Matamoros S, Cani PD, et al. Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity. Proc Natl Acad Sci U S A 2014; 111:E4485-E4493.
24. Chen P, Torralba M, Tan J, et al. Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice. Gastroenterology 2015; 148:203-214.
25. Moran CP, Shanahan F. Gut microbiota and obesity: role in aetiology and potential therapeutic target. Best Pract Res Clin Gastroenterol 2014; 28:585-597.
26. El Aidy S, Merrifield CA, Derrien M, et al. The gut microbiota elicits a profound metabolic reorientation in the mouse jejunal mucosa during conventionalisation. Gut 2013; 62:1306-1314.
27. Larsson E, Tremaroli V, Lee YS, et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut 2012; 61:1124-1131.
28. Buchwald H, Oien DM. Metabolic/bariatric surgery worldwide 2011. Obes Surg 2013; 23:427-436.
29. Kuipers F, Groen AK. FXR: the key to benefits in bariatric surgery? Nat Med 2014; 20:337-338.
30. Osto M, Abegg K, Bueter M, et al. Roux-en-Y gastric bypass surgery in rats alters gut microbiota profile along the intestine. Physiol Behav 2013; 119:92-96.
31. Liou AP, Paziuk M, Luevano JM, et al. Conserved shifts in the gut microbiota due to gastric bypass reduce host weight and adiposity. Sci Transl Med 2013; 5:178ra141.
32. Schauer PR, Kashyap SR, Wolski K, et al. Bariatric surgery versus intensive medical therapy in obese patients with diabetes. N Engl J Med 2012; 366:1567-1576.
33. Myronovych A, Kirby M, Ryan KK, et al. Vertical sleeve gastrectomy reduces hepatic steatosis while increasing serum bile acids in a weight-loss-independent manner. Obesity 2014; 22:390-400.
34. Begley M, Gahan CG, Hill C. The interaction between bacteria and bile. FEMS Microbiol Rev 2005; 29:625-651.
35. Vavassori P, Mencarelli A, Renga B, et al. The bile acid receptor FXR is a modulator of intestinal innate immunity. J Immunol 2009; 183:6251-6261.
36. Schaap FG, Trauner M, Jansen PL. Bile acid receptors as targets for drug development. Nat Rev Gastroenterol Hepatol 2014; 11:55-67.
37. Swann JR, Want EJ, Geier FM, Spagou K, et al. Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. Proc Natl Acad Sci U S A 2011; 108 (Suppl 1):4523-4530.
38. Vaquero J, Monte MJ, Dominguez M, et al. Differential activation of the human farnesoid X receptor depends on the pattern of expressed isoforms and the bile acid pool composition. Biochem Pharmacol 2013; 86:926-939.
39. Sayin SI, Wahlstrom A, Felin J, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 2013; 17:225-235.
40. Jones BV, Begley M, Hill C, et al. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 2008; 105:13580-13585.
41. Vrieze A, Out C, Fuentes S, et al. Impact of oral vancomycin on gut microbiota, bile acid metabolism, and insulin sensitivity. J Hepatol 2014; 60:824-831.
42. Islam KB, Fukiya S, Hagio M, et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 2011; 141:1773-1781.
43. Ryan KK, Tremaroli V, Clemmensen C, et al. FXR is a molecular target for the effects of vertical sleeve gastrectomy. Nature 2014; 509:183-188.
44. Joyce SA, MacSharry J, Casey PG, et al. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proc Natl Acad Sci U S A 2014; 111:7421-7426.
45. Vrieze A, Van Nood E, Holleman F, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012; 143:913-916; e917.
46. Romanos J, Rosen A, Kumar V, et al. Improving coeliac disease risk prediction by testing non-HLA variants additional to HLA variants. Gut 2014; 63:415-422.
47. Marild K, Stephansson O, Montgomery S, et al. Pregnancy outcome and risk of celiac disease in offspring: a nationwide case-control study. Gastroenterology 2012; 142:39-45; e33.
48. Marild K, Ye W, Lebwohl B, et al. Antibiotic exposure and the development of coeliac disease: a nationwide case-control study. BMC Gastroenterol 2013; 13:109.
49. Stene LC, Honeyman MC, Hoffenberg EJ, et al. Rotavirus infection frequency and risk of celiac disease autoimmunity in early childhood: a longitudinal study. Am J Gastroenterol 2006; 101:2333-2340.
50. Ivarsson A, Hernell O, Stenlund H, Persson LA. Breast-feeding protects against celiac disease. Am J Clin Nutr 2002; 75:914-921.
51. Szajewska H, Chmielewska A, Piescik-Lech M, et al. Systematic review: early infant feeding and the prevention of coeliac disease. Aliment Pharmacol Ther 2012; 36:607-618.
52. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009; 9:313-323.
53. de Meij TG, Budding AE, Grasman ME, et al. Composition and diversity of the duodenal mucosa-associated microbiome in children with untreated coeliac disease. Scand J Gastroenterol 2013; 48:530-536.
54. Collado MC, Donat E, Ribes-Koninckx C, et al. Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. J Clin Pathol 2009; 62:264-269.
55. Nadal I, Donat E, Ribes-Koninckx C, et al. Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol 2007; 56:1669-1674.
56. Nistal E, Caminero A, Herran AR, et al. Differences of small intestinal bacteria populations in adults and children with/without celiac disease: effect of age, gluten diet, and disease. Inflamm Bowel Dis 2012; 18:649-656.
57. Cheng J, Kalliomaki M, Heilig HG, et al. Duodenal microbiota composition and mucosal homeostasis in pediatric celiac disease. BMC Gastroenterol 2013; 13:113.
58. Di Cagno R, De Angelis M, De Pasquale I, et al. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol 2011; 11:219.
59. Wacklin P, Laurikka P, Lindfors K, et al. Altered duodenal microbiota composition in celiac disease patients suffering from persistent symptoms on a longterm gluten-free diet. Am J Gastroenterol 2014; 109:1933-1941.
60. Wacklin P, Kaukinen K, Tuovinen E, et al. The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestation of the disease. Inflamm Bowel Dis 2013; 19:934-941.
61. Arpaia N, Campbell C, Fan X, et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013; 504:451-455.
62. Olivares M, Neef A, Castillejo G, et al. The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease. Gut 2014. [Epub ahead of print]
63. Shanahan F, Quigley EM. Manipulation of the microbiota for treatment of IBS and IBD-challenges and controversies. Gastroenterology 2014; 146:1554-1563.
64. Nguyen HT, Dalmasso G, Muller S, et al. Crohn's disease-associated adherent invasive Escherichia coli modulate levels of microRNAs in intestinal epithelial cells to reduce autophagy. Gastroenterology 2014; 146:508-519.
65. Tougaard P, Skov S, Pedersen AE, et al. TL1A regulates TCRgammadelta intraepithelial lymphocytes and gut microbial composition. Eur J Immunol 2014. [Epub ahead of print]
66. Gevers D, Kugathasan S, Denson LA, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014; 15:382-392.
67. Haberman Y, Tickle TL, Dexheimer PJ, et al. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest 2014; 124:3617-3633.
68. Sommer F, Backhed F. The gut microbiota engages different signaling pathways to induce Duox2 expression in the ileum and colon epithelium. Mucosal Immunol 2014. [Epub ahead of print]
69. De Cruz P, Kang S, Wagner J, et al. Specific mucosa-associated microbiota in Crohn's disease at the time of resection are associated with early disease recurrence: a pilot study. J Gastroenterol Hepatol 2014. [Epub ahead of print]
70. Dey N, Soergel DA, Repo S, Brenner SE. Association of gut microbiota with postoperative clinical course in Crohn's disease. BMC gastroenterology 2013; 13:131.
71. Young VB, Raffals LH, Huse SM, et al. Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis. Microbiome 2013; 1:9.
72. Shen B. Acute and chronic pouchitis: pathogenesis, diagnosis and treatment. Nat Rev Gastroenterol Hepatol 2012; 9:323-333.
73. Tyler AD, Knox N, Kabakchiev B, et al. Characterization of the gut-associated microbiome in inflammatory pouch complications following ileal pouch-anal anastomosis. PLoS One 2013; 8:e66934.
74. Persborn M, Gerritsen J, Wallon C, et al. The effects of probiotics on barrier function and mucosal pouch microbiota during maintenance treatment for severe pouchitis in patients with ulcerative colitis. Aliment Pharmacol Ther 2013; 38:772-783.
75. Mar JS, Nagalingam NA, Song Y, et al. Amelioration of DSS-induced murine colitis by VSL#3 supplementation is primarily associated with changes in ileal microbiota composition. Gut Microbes 2014; 5:494-503.